Minimum information about marine microbial sampling

The Micro B3 checklist is a multi-disciplinary standard developed by the Micro B3 Consortium for description of marine microbial sampling. Content of the standard is grouped into six categories covering various aspects of marine microbial sampling. These categories are environment, measurement, sampling, event, sample and organism. Full adoption of the standard allows generation of data records, which are MIxS compliant but also compliant to minimal reporting requirements of the oceanographic and marine biodiversity community, i.e. respectively the Common Data Index (CDI) and the OBIS schema, advancing the metadata interoperability across research domains. Nucleotide sequences of marine microbial samples described according to the Micro B3 checklist can be placed into a very rich environmental context.

The MicroB3 checklist will facilitate description of samples collected during the Ocean Sampling Day OSD, a simultaneous sampling campaign of the world’s oceans to reveal a marine microbial diversity.

MicroB3 checklist

MANDATORY information

The Micro B3 checklist is schematically shown in the figure below. Mandatory information is placed in colour-coded triangles representing the above mentioned six categories of marine microbial sampling. Detailed description of the mandatory information can be found here. Marine microbial samples described with these mandatory fields are Micro B3 compliant.

RECOMMENDED information

In order to reach compliance with standards of all three scientific communities, the genomic (MIxS), oceanographic (CDI) and marine biodiversity (OBIS), Micro B3-recommended information needs to be provided for each sample. The Micro B3-recommended information should be submitted to the appropriate National Oceanographic Data Centre and for the OSD data to the PANGAEA. A comprehensive description of the Micro B3-recommended information for reaching full cross-domain compliance can be found here.

The Micro B3 consortium identified in close collaboration with the oceanographic and marine ecosystem biology communities a number of environmental parameters particularly valuable for description of the environmental context of marine microbial samples. A comprehensive description of these environmental parameters can be found here.

Micro B3 data submission

Submission of NON-GENOMIC data

The European Nucleotide Archive can accept molecular data and contextual data of marine microbial samples associated with genomic data.

Non-genomic data, i.e. oceanographic environmental data and morphology-based biodiversity data, should be submitted to the appropriate National Oceanographic Data Centre (NODC) according to established reporting practices maintained by oceanographic community experts. Major National Oceanographic Data Centres from countries bordering the North-East Atlantic, and its adjacent seas: the Mediterranean, the Black Sea, the Baltic, the North Sea and the Arctic are listed here.

Submission of GENOMIC data

Instructions for submissions of raw reads from marine microbial samples can be found here. Instructions for submissions of assembled and annotated sequences of marine microbial samples can be found here.

Contextual data of marine microbial samples associated with genomic data can be submitted to the European Nucleotide Archive using the ENA Micro B3 checklist available from the Webin submission tool.

Webin submission of an environmental Micro B3-compliant sample metadata is in detail described in the online video tutorial available here.

Submitters using the ENA Micro B3 checklist will need to provide the Micro B3 mandatory information but can also add user-defined attributes or use the optional MIxS terms clustered in the checklist into the following groups, (1) environmental conditions, (2) concentration measurements, (3) MIxS sample collection terms, (4) MIxS non-sample terms, (5) MIxS other attributes.

MANDATORY Micro B3 sample checklist

Recommendation applies to microbial sampling in the pelagic zone.

Field

Description

Controlled vocabulary/format*

Example

SAMPLING_ Campaign

Refers to a finite or indefinite activity aiming at collecting data/samples, e.g. a cruise, a time series, a mesocosm experiment.

Free text

OSD-SS2014

SAMPLING_Site

Refers to the unique identifier and name of the site/station where the data/sample collection is performed.

Format: <Site ID from OSD Site Registry>, <Site name from OSD Site Registry>

OSD5, Poseidon-E1-M3A Time Series Station

SAMPLING_Platform

Refers to the specific unique stage from which the sampling device was deployed; includes the platform category and platform name.

Format:<Platform category from SDN:L06>,<Platform name>

research vessel, FILIA

EVENT_Date/Time

Date and time when the sampling event started and ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event.

Date and time in UTC;
Format: yyyy-mm-ddThh:mm:ssZ

2013-06-21T14:05:00Z/2013-06-21T14:46:00Z

EVENT_Longitude

Longitude of the location where the sampling event started and ended, e.g. each CTD cast, net tow, or bucket collection is a distinct event